streptomyces/ripper repository overview

⁠RiPPer version 1.2

⁠Pull the docker image

docker pull streptomyces/ripper

⁠Get a container

Below, the environment variable NCBI_API_KEY in the host environment is being added to the container environment and, NCBI_API_EMAIL is being explicitly set in the container environment to the email address specified.

docker run --rm -it -v $PWD:/home/mnt \
-v $HOME/databases/pfam:/mnt/pfam \
--env NCBI_API_KEY
--env NCBI_API_EMAIL=<your@email> \
streptomyces/ripper

If you do not have an NCBI API key then remove that part from the command. NCBI_API_EMAIL is required and has to be provided.

Do not change the /home/mnt part or the /mnt/pfam part. /home/mnt refers to a directory in the container and scripts in the container expect to find this directory. The host directory you mount on /home/mnt in the container is where the output directories and files are written to. You can place your input list in the mounted host directory on the host side and access it in /home/mnt/ on the container side. See the example Run on your own list below.

⁠The Pfam-A database

This image does not include the Pfam-A database which is needed to run the analyses. Including it would make the image very big and it will be difficult to keep the database updated to the latest release.

Your directory which appears as /mnt/pfam on the container side should contain the Pfam database inside a directory named pfam.

From inside a running container you could make the database by stepping through the commands below. This needs to be done only once everytime the Pfam-A models are updated.

# Make sure that /mnt/pfam on the container side is bound to a
# directory on the host side.
cd /mnt/pfam
wget \
'https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz'
gunzip Pfam-A.hmm.gz
hmmpress Pfam-A.hmm
cd /home/work/

The above should result in the following files in /mnt/pfam/.

Pfam-A.hmm
Pfam-A.hmm.h3f
Pfam-A.hmm.h3i
Pfam-A.hmm.h3m
Pfam-A.hmm.h3p

⁠Carrying out an analysis in the running container

To ensure that ripper_run is working correctly, you can run a small test analysis on the accessions that are included in a test file named minitest.txt. There is also a microtest.txt which has just the top three lines of minitest.txt.

./ripper_run microtest.txt
./ripper_run minitest.txt

⁠Run on your own list

Use the following command to analyse your own list, substituting in a relevant filename for te_accessions.txt:

./ripper_run /home/mnt/te_accessions.txt

⁠Options

The defaults of some options are mentioned below.

--minPPlen             =      20;
--maxPPlen             =     120;
--prodigalScoreThresh  =     7.5;
--maxDistFromTE        =    8000;
--fastaOutputLimit     =       3;
--sameStrandReward     =       5;
--flankLen             =   40000;
--scan_signif_thresh   =    0.05;

These can be changes when invoking ripper_run. For example, to change the maximum distance from the TE to the precursor peptide (maxDistFromTE) --maxDistFromTE 7000 can be used. Note that capitalisation is significant. All lower-case form of the option should also work but wrong mixture of upper and lower case will not work.

Two other options are --ncbiapikey and --email both of which are unset by default (unless provided as environment variables at the time of instantiating the container). If you provide these then the values are sent along with requests to NCBI and they use these for the analysis of the usage of their services. It is best to provide these as environment variables (see Get a container above) so you need not use these options.

⁠Output files

The output consists of genbank files in the folder orgnamegbk. There should be one genbank file for each protein accession for which a genbank file was successfully retrieved from Genbank. The output of egn_ni.pl is in the folder named pna.